X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Febi%2FEBIFetchClient.java;h=3eef460bc9bb8f46ae803fa8c2889ff27373271b;hb=c932f0e85a8852824cdd8ce790af68682732c85c;hp=55315129a27d14fa837380abac4c715f8f4b0edb;hpb=30b2b47cbdfa35b127b0fb09e911815cddd9ed7b;p=jalview.git

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 5531512..3eef460 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -20,15 +20,18 @@
  */
 package jalview.ws.ebi;
 
+import java.util.Locale;
+
 import jalview.datamodel.DBRefSource;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
-import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileOutputStream;
+import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
@@ -90,8 +93,8 @@ public class EBIFetchClient
    *          the query formatted as db:query1;query2;query3
    * @param format
    *          the format wanted
-   * @param extension
-   *          for the temporary file to hold response
+   * @param ext
+   *          for the temporary file to hold response (without separator)
    * @return the file holding the response
    * @throws OutOfMemoryError
    */
@@ -102,7 +105,7 @@ public class EBIFetchClient
     File outFile = null;
     try
     {
-      outFile = File.createTempFile("jalview", ext);
+      outFile = File.createTempFile("jalview", "." + ext);
       outFile.deleteOnExit();
       fetchData(ids, format, outFile);
       if (outFile.length() == 0)
@@ -133,13 +136,14 @@ public class EBIFetchClient
     String database = parseIds(ids, querystring);
     if (database == null)
     {
-      System.err.println("Invalid Query string : '" + ids + "'");
-      System.err.println("Should be of form 'dbname:q1;q2;q3;q4'");
+      jalview.bin.Console.errPrintln("Invalid Query string : '" + ids + "'");
+      jalview.bin.Console.errPrintln("Should be of form 'dbname:q1;q2;q3;q4'");
       return null;
     }
 
     // note: outFile is currently always specified, so return value is null
-    String[] rslt = fetchBatch(querystring.toString(), database, format, outFile);
+    String[] rslt = fetchBatch(querystring.toString(), database, format,
+            outFile);
 
     return (rslt != null && rslt.length > 0 ? rslt : null);
   }
@@ -191,69 +195,83 @@ public class EBIFetchClient
    * @param database
    * @param format
    * @param outFile
-   * @return
+   * @return array of lines from EBI only if outFile is null (which it will not
+   *         be)
    * @throws OutOfMemoryError
    */
   String[] fetchBatch(String ids, String database, String format,
           File outFile) throws OutOfMemoryError
   {
-    // long time = System.currentTimeMillis();
     String url = buildUrl(ids, database, format);
-
+    InputStream is = null;
+    BufferedReader br = null;
     try
     {
       URL rcall = new URL(url);
-
-      InputStream is = new BufferedInputStream(rcall.openStream());
-      if (outFile != null)
+      HttpURLConnection conn = (HttpURLConnection) rcall.openConnection();
+      int responseCode = conn.getResponseCode();
+      if (responseCode == 200)
       {
-        FileOutputStream fio = new FileOutputStream(outFile);
-        // fio.write("<?xml version='1.0' encoding='UTF-8'?>\n".getBytes());
-        byte[] bb = new byte[32 * 1024];
-        int l;
-        while ((l = is.read(bb)) > 0)
+        is = conn.getInputStream();
+        if (outFile != null)
         {
-          fio.write(bb, 0, l);
+          Platform.streamToFile(is, outFile);
+          return null;
         }
-        fio.close();
-        is.close();
-      }
-      else
-      {
-        BufferedReader br = new BufferedReader(new InputStreamReader(is));
+        br = new BufferedReader(new InputStreamReader(is));
         String rtn;
-        List<String> arl = new ArrayList<String>();
+        List<String> arl = new ArrayList<>();
         while ((rtn = br.readLine()) != null)
         {
           arl.add(rtn);
         }
-        return arl.toArray(new String[arl.size()]);
+        return (String[]) arl.toArray();
       }
+      jalview.bin.Console.errPrintln(
+              "Warning: response code " + responseCode + " for " + url);
     } catch (OutOfMemoryError er)
     {
-      System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + database
+      jalview.bin.Console.outPrintln("OUT OF MEMORY DOWNLOADING QUERY FROM " + database
               + ":\n" + ids);
       throw er;
     } catch (Exception ex)
     {
-      if (ex.getMessage().startsWith(
+      if (!ex.getMessage().startsWith(
               "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
       {
-        return null;
+        jalview.bin.Console.errPrintln("Unexpected exception when retrieving from "
+                + database + "\nQuery was : '" + ids + "'");
+        ex.printStackTrace(System.err);
       }
-      System.err.println("Unexpected exception when retrieving from "
-              + database
-              + "\nQuery was : '" + ids + "'");
-      ex.printStackTrace(System.err);
-      return null;
     } finally
     {
-      // System.err.println("EBIFetch took " + (System.currentTimeMillis() -
-      // time) + " ms");
+      if (is != null)
+      {
+        try
+        {
+          is.close();
+        } catch (IOException e)
+        {
+        }
+      }
+      if (br != null)
+      {
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+        }
+      }
     }
     return null;
   }
 
+  static
+  {
+    Platform.addJ2SDirectDatabaseCall("https://www.ebi.ac.uk/");
+  }
+
   /**
    * Constructs the URL to fetch from
    * 
@@ -268,13 +286,14 @@ public class EBIFetchClient
     if (database.equalsIgnoreCase(DBRefSource.EMBL)
             || database.equalsIgnoreCase(DBRefSource.EMBLCDS))
     {
-      url = "http://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase()
-              + (format != null ? "&" + format : "");
+      url = "https://www.ebi.ac.uk/ena/browser/api/embl/"
+              + ids.toLowerCase(Locale.ROOT) + "?download=true&gzip=true";
     }
     else
     {
-      url = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
-              + database.toLowerCase() + "/" + ids.toLowerCase()
+      url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
+              + database.toLowerCase(Locale.ROOT) + "/"
+              + ids.toLowerCase(Locale.ROOT)
               + (format != null ? "/" + format : "");
     }
     return url;